MolNFT v1 · #176282 · protein
Vibrio vulnificus wzb in complex with benzylphosphonate
7DHE · Protein-tyrosine-phosphatase: “Vibrio vulnificus wzb in complex with benzylphosphonate”. X-ray diffraction, 1 ligand (B85), 2 pockets (best druggability 0.76). MolNFT v1 #176282 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7DHE
- Type
- protein
- Length
- 585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine-phosphatase
- EC
- 3.1.3.48
- UniProt
- E5F0S0
- Ligands
- B85
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Protein-tyrosine-phosphatase (EC 3.1.3.48) | protein | 146 | 43% helix, 14% strand | E5F0S0 |
| B | Protein-tyrosine-phosphatase (EC 3.1.3.48) | protein | 147 | 43% helix, 15% strand | E5F0S0 |
Ligands and binding sites
- B85 · benzylphosphonic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.76 | 0.78 | 86 | empty |
| 2 | 58 | 0.51 | 0.86 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 671 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 299 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 285 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7DHE · Vibrio vulnificus Wzb in complex with benzylphosphonate · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E5F0S0
- Elsewhere: RCSB PDB 7DHE · PDBe 7DHE · UniProt E5F0S0
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